kegg-database

Query KEGG biological pathways and gene mappings via its REST API.

8|Updated Nov 19, 2025

Search Tags:#bioinformatics #pathway analysis #gene mapping #drug interactions #kegg #metabolic pathways

Ready to run

npx skills add https://github.com/sanand0/scientific-research --skill kegg-database-sanand0

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/sanand0/scientific-research/tree/main/.claude/skills/kegg-database
Command: npx skills add https://github.com/sanand0/scientific-research --skill kegg-database-sanand0

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides direct access to the KEGG database, enabling users to query biological pathways, gene-pathway mappings, metabolic pathways, drug interactions, and perform ID conversions for academic research.

Core Features & Use Cases

Pathway Analysis: Retrieve and analyze metabolic, genetic, cellular, and disease pathways.
Gene/Compound Mapping: Map genes to pathways, compounds to reactions, and perform ID conversions between KEGG and external databases (e.g., UniProt, PubChem).
Drug Interaction Data: Access information on drug-drug interactions.
Use Case: A researcher needs to find all human genes associated with the 'Glycolysis' pathway and then retrieve the protein sequences for those genes.

Quick Start

Use the kegg-database skill to find all human pathways linked to the gene 'hsa:10458'.

Frequently Asked Questions about kegg-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I map genes to metabolic pathways using the KEGG REST API?▼

Gene mapping to KEGG metabolic pathways is done by querying the KEGG REST API using Python helper functions. You can retrieve gene-pathway mappings and link specific gene identifiers, such as 'hsa:10458', to their associated biological pathways.

Can I convert external database IDs to KEGG identifiers for pathway analysis?▼

Cross-database ID conversions between KEGG and external databases like UniProt or PubChem are supported. The Skill utilizes direct REST API operations to translate external identifiers into KEGG format for academic pathway analysis.

How do I retrieve drug interaction data from the KEGG database?▼

Drug interaction data is accessible via programmatic queries to the KEGG REST API. You can look up drug-drug interactions and retrieve compound information by calling the provided Python helper functions.

What biological pathway types can I analyze with this KEGG database tool?▼

You can retrieve and analyze metabolic, genetic, cellular, and disease pathways. The Skill provides direct access to the KEGG database to support detailed pathway analysis and gene annotation for academic research.

Do I need to install external dependencies to access KEGG pathways programmatically?▼

No external dependencies are required to access KEGG pathways. The Skill operates using included Python scripts and reference components to execute direct REST API queries against the KEGG database.

How do I find human genes associated with a specific pathway like Glycolysis?▼

Finding human genes associated with Glycolysis involves querying the KEGG REST API for pathway-gene mappings. The Python helper functions retrieve all genes linked to the specified pathway identifier for subsequent sequence analysis.